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- PDB-1arz: ESCHERICHIA COLI DIHYDRODIPICOLINATE REDUCTASE IN COMPLEX WITH NA... -

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Basic information

Entry
Database: PDB / ID: 1arz
TitleESCHERICHIA COLI DIHYDRODIPICOLINATE REDUCTASE IN COMPLEX WITH NADH AND 2,6 PYRIDINE DICARBOXYLATE
ComponentsDIHYDRODIPICOLINATE REDUCTASE4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / REDUCTASE / LYSINE BIOSYNTHESIS / NADH BINDING
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / amino acid biosynthetic process / NAD binding / NADP binding / identical protein binding / cytosol
Similarity search - Function
Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / PYRIDINE-2,6-DICARBOXYLIC ACID / PHOSPHATE ION / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsScapin, G. / Reddy, S.G. / Zheng, R. / Blanchard, J.S.
Citation
Journal: Biochemistry / Year: 1997
Title: Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate.
Authors: Scapin, G. / Reddy, S.G. / Zheng, R. / Blanchard, J.S.
#1: Journal: Biochemistry / Year: 1995
Title: Three-Dimensional Structure of Escherichia Coli Dihydrodipicolinate Reductase
Authors: Scapin, G. / Blanchard, J.S. / Sacchettini, J.C.
#2: Journal: Biochemistry / Year: 1995
Title: Expression, Purification, and Characterization of Escherichia Coli Dihydrodipicolinate Reductase
Authors: Reddy, S.G. / Sacchettini, J.C. / Blanchard, J.S.
History
DepositionAug 8, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2013Group: Non-polymer description
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDRODIPICOLINATE REDUCTASE
B: DIHYDRODIPICOLINATE REDUCTASE
C: DIHYDRODIPICOLINATE REDUCTASE
D: DIHYDRODIPICOLINATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,84513
Polymers115,1754
Non-polymers2,6719
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16850 Å2
ΔGint-58 kcal/mol
Surface area40270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.600, 123.800, 66.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.929353, -0.055267, -0.365033), (-0.065331, -0.94851, 0.309937), (-0.363367, 0.311889, 0.877889)131.35381, 81.1805, 12.0157
2given(0.873517, 0.380367, 0.303791), (0.378613, -0.923116, 0.067147), (0.305975, 0.056365, -0.950369)-12.8172, 55.7706, 9.81
3given(-0.944528, -0.322212, 0.06361), (-0.322031, 0.87054, -0.372096), (0.064519, -0.37194, -0.926012)136.603, 32.0285, 42.8076
4given(-0.923552, -0.061842, -0.378453), (-0.061378, -0.950348, 0.305077), (-0.378528, 0.304983, 0.8739)131.6226, 81.0093, 13.7972
5given(-0.942638, -0.324274, 0.079246), (-0.33098, 0.87703, -0.348239), (0.043424, -0.354493, -0.93405)136.58189, 32.3025, 43.814

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DIHYDRODIPICOLINATE REDUCTASE / 4-hydroxy-tetrahydrodipicolinate reductase / DHPR


Mass: 28793.631 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cell line: BL21 / Gene: DAPB / Plasmid: PET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04036, EC: 1.3.1.26

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Non-polymers , 5 types, 188 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#5: Chemical ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID / Dipicolinic acid


Mass: 167.119 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H5NO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 23-26% PEG 8000, IN 160-180 MM POTASSIUM PHOSPHATE, 100 MM SODIUM CACODYLATE PH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
123-26 %PEG80001reservoir
2160-180 mMpotassium phosphate1reservoir
3100 mMsodium cacodylate1reservoirpH6.5
420 mg/mlprotein1drop
52 mMNADH1drop
630 mMPDC1drop

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1996
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 32245 / % possible obs: 90 % / Observed criterion σ(I): 0.5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Rsym value: 0.081 / Net I/σ(I): 15.9
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 2 / Rsym value: 0.269 / % possible all: 74
Reflection
*PLUS
Num. measured all: 119624 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 74 % / Num. unique obs: 4365 / Num. measured obs: 8022 / Rmerge(I) obs: 0.269

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DIH

1dih


Resolution: 2.6→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 1.0E-5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 -5 %RANDOM
Rwork0.214 ---
obs0.214 32222 89.9 %-
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.99 Å20 Å20 Å2
2---0.71 Å20 Å2
3----2.28 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7878 0 175 179 8232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.416 -5 %
Rwork0.32 2474 -
obs--72 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7
LS refinement shell
*PLUS
Rfactor Rwork: 0.32

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